facile synthesis, characterization and in silico docking
TRANSCRIPT
Rwanda Journal of Engineering, Science, Technology and Environment, Volume 4, Issue 1, June 2021
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Facile Synthesis, Characterization and in Silico Docking Studies of Novel
Thiazolidine-2,4-Dione-Based Mannich Base Bearing Furan/Thiophene
Moiety as Promising Anti-Inflammatory Agents
Jean Baptiste Nkurunziza1*, Pierre Dukuziyaturemye2, Edith Musabwa 2, Balakrishna Kalluraya3
1Department of Mathematics, Science and Physical Education, College of Education, University of Rwanda,
P.O.Box: 55 Rwamagana, Rwanda 2Department of Environmental Health Sciences, College of Medicine and Health Sciences, University of Rwanda,
P.O.Box 3286, Kigali, Rwanda 3Department of Studies in Chemistry, Mangalore University, Mangalagangothri-574199, Karnataka, India.
*Corresponding Author: [email protected]
DOI: 10.4314/rjeste.v4i1.5
https://dx.doi.org/10.4314/rjeste.v4i1.5
Abstract
Mannich bases are compounds bearing a β-amino carbonyl moiety. They are formed in the
Mannich reaction that consists of an amino alkylation of an acidic proton placed next to a
carbonyl functional group by formaldehyde and a primary or secondary amine. Mannich base
products are known for their curative properties such as anti-inflammatory, antibacterial,
anticancer, antifungal, anthelmintic, anticonvulsant, analgesic, anti-HIV, antipsychotic, antiviral,
and antimalarial activities. Further, thiazolidinedione derivatives have shown to be efficacious in
inflammatory diseases as wide-ranging as psoriasis, ulcerative colitis and non-alcoholic
steatohepatitis. In light of the above observations, new series of thiazolidine-2,4-dione based
Mannich base derivatives were synthesized via a simple and catalyst-free procedure involving
the condensation of thiazolidine-2,4-dione, formaldehyde and secondary amines in DMF solvent.
The structures of the newly synthesized compounds were confirmed by their IR, 1H-NMR, and
Mass spectra. The synthesized compounds were tested for their in silico anti-inflammatory
activity by Docking studies against COX-2 enzyme (PDB: 1CX2). Compounds 4a and 4b
showed good in silico anti-inflammatory properties comparable to that of standard drug
Diclofenac and may be considered as promising candidates for the development of new anti-
inflammatory agents.
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Keywords: Anti-inflammatory agents; Docking studies; Furan; Thiazolidine-2,4-dione;
Thiophene.
1. Introduction
Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used in the treatment and
management of inflammation and pain associated with conditions such as osteoarthritis,
rheumatoid arthritis, post-operative pain, orthopedic injuries, ankylosing spondylitis, gout,
dysmenorrhea, dental pain and headache (Atzeni et al., 2018; Ong et al., 2007). Non-steroidal
anti-inflammatory drugs are divided into two categories: non-selective inhibiting both
cyclooxygenase enzymes COX-1 and COX-2, and selective inhibiting COX-2 enzyme (Brune
and Patrignani, 2015). Although COX-1 and COX-2 are isoenzymes involved in the same
physiological pathway converting arachidonic acid (AA) to prostaglandins (PDs) (Bakhle, 1999;
Meek et al., 2010), COX-1 isoenzyme is a constitutive enzyme mainly found in the
gastrointestinal lining with a “house-keeping” role in regulating many normal physiological
processes in which prostaglandins serve a protective role (Fokunang et al., 2018), though COX-2
enzyme is facultative, and expressed at the sites of inflammation by pro-inflammatory molecules
such as interleukin-1 (IL-1), tumor necrosis factor- (TNF-), lipopolysaccharide (LPS), and tissue
plasminogen activator (TPA) (Fokunang et al., 2018; B Bari and D Firake, 2016) and produces
the desirable effects of NSAIDs (Zarghi and Arfaei, 2011). For the reasons stated above, long
term uses of non-selective NSAIDs is not advisable due to their severe gastrointestinal toxicities
(Rodríguez and González-Pérez, 2005; Vostinaru, 2017), resulting from their stronger inhibition
of COX-1 enzyme (Vostinaru, 2017). Examples of NSAIDs that were removed from the market
due to their toxicities include Vioxx (rofecoxib) pulled from the worldwide market due to its
increased risk for heart attacks and strokes (Sibbald, 2004); Bromfenac, Ibufenac, and
Benoxaprofen that were reported to be hepatotoxic (Goldkind, 2006). Therefore, the present
work intends to search for novel safe and selective COX-2 inhibitors for the management of pain
and inflammation.
Thiazolidine-2,4-dione (TZD) derivatives were reported to exhibit diverse pharmacological
properties such as anti-tubercular (Chilamakuru et al., 2013), antidiabetic, antimicrobial and anti-
cancer (Durai Ananda Kumar et al., 2015). Recently, it was reported that TZD derivatives are
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potent anti-inflammatory agents (Srivastava et al., 2019). In the study conducted by Zhu et al.
(2011), TZDs inhibited the release of a variety of inflammatory mediators from human Airway
Smooth Muscle cells, suggesting their uses in the treatment of asthma. Ceriello (2007) reviewed
the anti-inflammatory activity of TZDs and found that these compounds act by modulating the
anti-inflammatory markers such as IL-6, IL-18, CRP, MMP-2, MMP-9. Mohanty et al. (2004)
evidenced the anti-inflammatory effect of rosiglitazone as a drug of the thiazolidinedione class
that exerts an anti-inflammatory effect at the cellular and molecular level, and in plasma. In
addition to these useful properties of thiazolidinedione products; furan and thiophene derivatives
form a class of compounds with a broad spectrum of biological properties such as antibacterial
(Holla et al., 1987), anti-allergic, antidepressant, antidiabetic, analgesic and anti-inflammatory
activities (Mishra et al., 2011).
Nowadays, in silico molecular docking studies of small molecules to protein binding sites has
become an increasingly popular approach for the development of new drugs (Berry et al., 2015).
This is because in silico molecular docking study requires very less time to differentiate from
many compounds the most probable potent ones with desired biological activities when
compared with traditional laboratory experiments (Naim et al., 2018; Afriza et al., 2018). In view
of the above prominent properties of thiazolidinedione, furan and thiophene derivatives and rapid
with higher precision of in silico docking studies, novel series of compounds incorporating both
thiazolidine-2,4-dione and furan/thiophene moieties in one Mannich base molecule that might
display synergetic and enhanced biological activities were synthesized, characterized and
evaluated for their in silico COX-2 inhibitory activity.
2. Material and methods
2.1. Material
The innovative DTC-967A apparatus was used to determine the melting points of the new
compounds and are uncorrected. The IR-spectra (in KBr pellets) were recorded on Shimadzu FT-
IR Prestige-21 spectrophotometer and are expressed in cm-1. The mass spectra were recorded on
Shimadzu LC-MS-8030 mass spectrophotometer operating at 70 eV. A Bruker AVANCE II 400
MHz instrument was used to record 1H-NMR spectra in CDCl3 as solvent and TMS as an
internal standard.
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2.2. Chemistry method
Thiazolidine-2,4-dione (1) was synthesized by the cyclocondensation of thiourea with
monochloroacetic acid in acidified water solvent (Kar et al., 2014). Knoevenagel condensation of
thiazolidine-2,4-dione (1) with furan/thiophene-5-carbaldehyde (2) in ethanol solvent containing
a catalytic amount of piperidine afforded the key intermediate: furfurylidene/thienylidene
thiazolidine-2,4-dione (3) prepared according to Ha et al. (2012). Novel Mannich base products
(4) were synthesized by reacting compounds (3) with formaldehyde and secondary amines:
piperidine, morpholine or N-methylpiperazine (Scheme 1) in DMF solvent as given in the
general procedure. The completion of the reaction, as well as the purity of the products (4), were
checked by TLC using silica gel plates (Merck) with hexane:ethylacetate (6:4) as mobile phase.
Scheme 1: Synthesis of Mannich base derivatives of thiazolidinedione
Synthesis of 5-(furan-2/thiophen-2-ylmethylene)thiazolidine-2,4-dione-based Mannich
bases (4a-e): General procedure
Furfurylidene/thienylidene thiazolidine-2,4-dione (3) (0.01 mol) and formaldehyde (40%, 1.5
mL) were added in 100 mL Erlenmeyer flask containing 10 mL DMF. Using a magnetic stirrer,
the mixture was stirred at room temperature for 20 min. An appropriate secondary amine (0.01
mol): piperidine / morpholine / N-methyl piperazine was then added, and the resulting mixture
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was further stirred at room temperature for 6 hours to precipitate Mannich base products that
were collected by filtration, washed with cold water, dried and recrystallized from ethanol.
2.3. Molecular Docking Studies
In silico docking study was performed according to Rizvi et al. (2013) to predict interactions of
newly synthesized compounds (4a-e) with the target COX-2 enzyme's active site. The crystal
structure of COX-2 (PDB code: 1CX2) was downloaded from RCSB Protein Data Bank
(http://www.rcsb.org) as 1CX2.PDB (gz). It was then processed using Discovery Studio Biovia
2020 suite (Dassault Systèmes, San Diego, California, USA) in which protein inhibitor SC558,
all water molecules, unwanted heteroatoms and similar chains B, C and D were deleted to
generate the file saved as 1CX2.PDB. This file was further processed by adding polar hydrogen
atoms and Kollman Charges to the individual protein atoms with Auto Dock Tool (ADT)
software to get 1CX2.PDBT file required for Autogrid and AutoDock (Huey and Morris, 2008);
Rizvi et al., 2013).
The Marvin Sketch software (Marvin suite 20.11.0) was used for drawing and energy
minimization of each ligand structure (4a-e) to generate ligand.PDB. The ADT was then used to
process these ligands in which nonpolar hydrogens were combined, Gasteiger changes and
rotatable bonds were added and generated ligand.PDBQT format needed by Autogrid and
Autodock (Rizvi et al., 2013; Morris, 2012). Autogrid parameters were set using ADT and a
docking grid box was built with 40, 40, and 40 points in X, Y and Z dimensions with X=31.594,
Y=24.653, and Z=12.650 as the position of the active site to generate a.GPF file. A docking
parameter file a.DPF was prepared using the Lamarckian genetic algorithm 4.2 search method
implemented in AutoDock 4.2 software integrated within Auto Dock Tools version 1.5.6 (ADT;
Scripps Research Institute, La Jolla, San Diego, USA). The receptor was kept rigid, ligands were
allowed to be flexible and all docking parameters were set to default. The molecular docking was
performed on Microsoft windows 10, 64-bit laptop using Cygwin software. The docking results
were analyzed by Discovery Studio Biovia 2020 suite software.
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3. Results and discussion
3.1. Chemistry
The structures of newly synthesized compounds 5-(furan-2/thiophen-2 ylmethylene)thiazolidine-
2,4-dione-based Mannich compounds (4a-e) were confirmed by their IR, 1H-NMR, and mass
spectra. Other data that characterize the newly synthesized compounds are given in Table 1.
Table 1: Characterization data of synthesized thiazolidinedione based Mannich bases (4a-e).
Compd.
No.
X Y M.P (oC)
(Yield %)
Molecular
formula
Mol. Wt Chemical structure
4a O CH2 189-191
(82)
C14H16N2O3S 292.35
4b S CH2 220-222
(74)
C14H16N2O2S2 308.41
4c S O 198-200
(76)
C13H14N2O3S2 310.39
4d S N-CH3 206-208
(72)
C14H17N3O3S 307.37
4e O O 176-178
(68)
C13H14N2O4S 294.33
The table above gives the melting point: M.P (oC), molecular formula, molecular weight (Mt),
and the chemical structure of the newly synthesized compounds 4a-4e. The results from the
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above table show that the newly synthesized compounds were formed in a good yield ranging
from 68% to 82% with molecular weight between 292 to 310.
The IR spectrum of 5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-2,4-dione (4a)
(Figure 1) showed prominent bands at 3089 cm-1 and 2964 cm-1 for C-H stretching frequencies.
The bands at 1645 cm-1 and 1589 cm-1 are attributed for C=O stretching frequencies, while the
C-O band appeared at 1273 cm-1 stretching frequency.
Figure 1: The IR spectrum of 5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-2,4-
dione (4a)
The formation of Mannich base products (4a-e) from compounds (3) was further confirmed by
their 1H NMR spectra. As a typical example, in the 1H-NMR (400 MHz, CDCl3) spectrum of 5-
(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-2,4-dione (4a) (Figure 2) the
protons at the 4th position of piperidine moiety labelled as HA appeared as a quintet at δ 1.33-1.39
ppm integrating for two protons. A quintet signal seen at δ 1.52-1.58 ppm is due to the resonance
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of four protons (HB) located at the 3rd position of piperidine moiety. The four protons (HC) from
the 2nd position of the piperidine group resonated as a triplet at δ 2.59-2.62 ppm while methylene
N-CH2-N protons (HD) came into resonance as a singlet at δ 4.69 ppm integrating for two
protons. One proton (HG) at the 4th position of furan ring come into resonance as a triplet at δ
6.57-6.58 ppm, whereas a doublet seen δ 6.77-6.78 ppm (J = 3.48 Hz) resulted from the
resonance of a proton (HF) located at the 3rd position of furan ring. The CH=C proton (HE)
resonated as a singlet at δ 7.62 ppm, and a proton (HI) at 5th position of furan ring appeared as a
doublet at δ 7.66-7.67 ppm (J = 1.64 Hz).
Figure 2: 1H NMR spectrum of 5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-
2,4-dione (4a).
The mass spectra further confirmed the structures of the new compounds (4a-e). In a typical
example, the mass spectrum of 5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-
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2,4-dione (4a) (Figure 3) showed molecular ion peak at m/z = 292 (M+) which is in conformity
with its molecular formula C14H16N2O3S.
Figure 3: Mass spectrum of of 5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-
2,4-dione (4a)
The spectral data of other newly synthesized compounds prepared according to the general
procedure presented in section 2.2 are given below:
4b) 3-(Piperidin-1-ylmethyl)-5-(thiophen-2-ylmethylene)thiazolidine-2,4-dione
IR (KBr, γ/cm-1): 3074, 2985 (C-H stretch), 1633, 1573 (C=O stretch), 1H-NMR (400 MHz,
CDCl3): δ (ppm) 1.34-1.40 (quintet, 2H at 4th position piperidine), 1.52-1.58 (quintet, 4H at 3rd
position of piperidine), 2.60-2.63 (t, 4H at 2nd position of piperidine), 4.71 (s, 2H, N-CH2-N),
7.17-7.20 (t, 1H, furan-4H), 7.39-7.40 (d, J=3.64 Hz, 1H, furan-3H), 7.64-7.66 (d, J=5.08 Hz,
1H, furan-5H), 8.04 (s, 1H, C=CH). LC-MS (m/z): 309 (M+ + 1).
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4c) 3-(Morpholinomethyl)-5-(thiophen-2-ylmethylene)thiazolidine-2,4-dione
IR (KBr, γ/cm-1): 3111, 2964 (C-H stretch), 1651, 1589 (C=O stretch), 1H-NMR (400 MHz,
CDCl3): δ (ppm) 2.66-2.68 (t, 4H adjacent to N-morpholine), 3.66-3.68 (t, 4H adjacent to O-
morpholine), 4.70 (s, 2H, N-CH2-N), 7.18-7.21 (t, 1H, furan-4H), 7.40-7.41 (d, J=3.68 Hz, 1H,
furan-3H), 7.66-7.67 (d, J=5.04 Hz, 1H, furan-5H), 8.06 (s, 1H, C=CH). LC-MS (m/z): 310
(M+).
4d) 5-(furan-2-ylmethylene)-3-((4-methylpiperazin-1-yl)methyl)thiazolidine-2,4-dione
IR (KBr, γ/cm-1): 3057, 2978 (C-H stretch), 1649, 1587 (C=O stretch), 1H-NMR (400 MHz,
CDCl3): δ (ppm) 2.25 (s, 3H, N-CH3), 2.41 (s, 4H of piperazine moiety), 2.72 (s, 4H of
piperazine moiety), 4.73 (s, 2H, N-CH2-N), 7.18-7.20 (t, 1H, furan-4H), 7.39-7.40 (d, J=3.72 Hz,
1H, furan-3H), 7.65-7.66 (d, J=5.00 Hz, 1H, furan-5H), 8.03 (s, 1H, C=CH). LC-MS (m/z): 323
(M+).
4e) 5-(furan-2-ylmethylene)-3-(morpholinomethyl)thiazolidine-2,4-dione
IR (KBr, γ/cm-1): 3082, 2985 (C-H stretch), 1637, 1577 (C=O stretch), 1H-NMR (400 MHz,
CDCl3): δ (ppm) 2.65-2.68 (t, 4H adjacent to N-morpholine), 3.66-3.68 (t, 4H adjacent to O-
morpholine), 4.68 (s, 2H, N-CH2-N), 6.58-6.59 (m, 1H, furan-4H), 6.78-6.79 (d, J=3.56 Hz, 1H,
furan-3H), 7.64 (s, 1H, C=CH), 7.64-7.68 (d, J=4.52 Hz, 1H, furan-5H). LC-MS (m/z): 294
(M+).
The plausible mechanism for the formation of the above new Mannich base products probably
involved the formation of an alcohol intermediate (OH-intermediate) rather than imine from the
reaction between thiazolidine-2,4-dione derivatives (3) with formaldehyde. This intermediate
product then condensed with secondary amines to furnish the title compounds (4) in the reaction
that has not required a catalyst (Scheme 2).
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Scheme 2: Mechanism for the formation of Mannich bases (4a-e)
3.2. Molecular Docking Study
In silico anti-inflammatory activity of compounds 4a-e was undertaken by studying the binding
and inhibition effects of ligands (4a-e) to the target COX-2 protein (PDB code: 1CX2) in which
the co-crystallized structure SC-558 was carefully removed using Discovery studio 2020 suite.
The docking results of the synthesized compounds (4a-e) and diclofenac used as the reference
drug are presented in Table 2.
Table 2. Docking results of thiazolidinedione-based Mannich base bearing furan/thiophene
moiety (4a-e).
Compound
No.
Binding
energy
Inhibitory
constant (μM)
No. of
H-bonds
H-Bond
4a -7.61 2.65 1 A:ARG120:HH::UNK0:O
4b -7.59 2.75 0 -
4c -6.64 13.53 1 A:TYR385:HH::UNK0:O
4d -6.72 11.81 0 -
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4e -6.95 8.03 1 A:ARG120:HH::UNK0:O
Diclofenac -7.63 2.53 1 A:ARG120:HH::UNK0:O
The above results showed that two compounds 4a and 4b displayed good binding energy of
-7.61 kJ mol-1 and -7.59 kJ mol-1 respectively, which are comparable to the reference drug
diclofenac with -7.63 kJ mol-1. In addition to one conventional hydrogen bond interaction
between the oxygen atom of furan moiety in the compound 4a with NH of ARG 120 and one
carbon-hydrogen bond between the nitrogen atom of piperidine moiety with a CH group of VAL
523, the observed high binding affinity of compound 4a has been attributed to strong
hydrophobic interactions between 4a ligand with VAL 116, VAL 349, LEU 359, LEU 531, MET
522 and ALA 527 amino acids that maximized its interactions with the target binding site
(Figure 4a and 4b).
(a) (b)
Figure 4(a): Docked complex between the protein 1CX2 and ligand 4a; Figure 4(b):
Interacting residues between the protein 1CX2 and ligand 4a. The hydrogen bonds between
one of the O-atoms of the ligand with ARG 120 is shown in green dotted line.
The 1CX2-Diclorofenac complex is given in Figure 5(a) and the interacting residues in the
same complex are shown in Fig 5(b). Diclofenac displayed one conventional hydrogen bond
between the oxygen atom of the ligand with NH of ARG 120, and also showed strong
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hydrophobic interactions with VAL 349, VAL 523, LEU352 and ALA 527 amino acids of the
target active site.
(a) (b)
Figure 5(a): Docked complex between protein 1CX2 and diclofenac ligand; Figure 5(b):
Interacting residues in 1CX2-Diclofenac complex. The hydrogen bond between one of the O-
atoms of the ligand with ARG 120 is shown in green dotted line. The observed results are in line
with Mousa et al. (2019) experiment in which Diclofenac inhibited the 1CX2 enzyme by binding
on ARG 120. Furthermore, molecular docking study results showed that each ligand molecule
displayed its own conformation, related to its IR spectrum that has fitted within the active site to
some extent. As a typical example, the IR spectrum of compound 4a showed the IR band at 1273
cm-1 for C-O-C (stretching) of the furan moiety. This furan-oxygen atom displayed one H-bond
with ARG 120 of the 1CX2 target protein. However, compound 4b which is lacking such a C-O-
C group of atoms did not display such IR band, hence unable to display any hydrogen bond with
the protein active site.
4. Conclusion
We successfully achieved the synthesis of novel series of thiazolidine-2,4-dione-based Mannich
base bearing furan/thiophene moiety (4a-e) in a reaction that did not require any acidic catalysts.
In silico docking studies of compounds (4a-e) on particular cyclooxygenase COX-2 enzyme
(PDB ID: 1CX2) have been evaluated in comparison with Diclofenac used as a reference drug.
The compounds 4a (5-(furan-2-ylmethylene)-3-(piperidin-1-ylmethyl)thiazolidine-2,4-dione)
and 4b (3-(Piperidin-1-ylmethyl)-5-(thiophen-2-ylmethylene)thiazolidine-2,4-dione) displayed
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comparable docking energy to that of standard drug Diclofenac, and the present molecular
docking studies suggested that these compounds 4a and 4b are candidate ligands for restoring
inflammation and pain in conditions such as osteoarthritis, rheumatoid arthritis.
Acknowledgement
The authors are thankful to the Head, USIC-Mangalore University and SAIF-Panjab University
for providing facilities for spectral data.
Conflict of interest
The authors declare no conflict of interest
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